Entering edit mode
Nenad Bartonicek
▴
20
@nenad-bartonicek-3296
Last seen 10.5 years ago
Hello,
There seems to be a problem in retrieving annotation from the chip
"affy_huex_1_0_st_v2".
>library(biomaRt)
>ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
#check if "affy_huex_1_0_st_v2" is a valid attribute
>attributes=listAttributes(ensembl)
>grep("affy_huex_1_0_st_v2",attributes[,1])
[1] 13
#collect data
>data=getBM(attributes="affy_huex_1_0_st_v2", mart=ensembl)
Error in postForm(paste(martHost(mart), "?", sep = ""), query =
xmlQuery) :
transfer closed with outstanding read data remaining
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices datasets tools utils
methods
[8] base
other attached packages:
[1] biomaRt_1.16.0 R.utils_1.1.1 R.oo_1.4.6
R.methodsS3_1.0.3
[5] Biobase_2.2.2
loaded via a namespace (and not attached):
[1] RCurl_0.94-1 XML_2.3-0
Thank you for your help,
Nenad
Nenad Bartonicek
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom
tel: +44-755-435-9057
[[alternative HTML version deleted]]